[English] 日本語
Yorodumi
- PDB-3uug: Crystal structure of the periplasmic sugar binding protein ChvE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uug
TitleCrystal structure of the periplasmic sugar binding protein ChvE
ComponentsMultiple sugar-binding periplasmic receptor ChvE
KeywordsSUGAR BINDING PROTEIN / periplasmic binding protein / SUGAR-BINDING PROTEIN / sugar / periplasmic
Function / homology
Function and homology information


chemotaxis / periplasmic space
Similarity search - Function
: / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranuronic acid / Multiple sugar-binding periplasmic receptor ChvE
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHu, X. / Zhao, J. / Binns, A. / Degrado, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Agrobacterium tumefaciens recognizes its host environment using ChvE to bind diverse plant sugars as virulence signals.
Authors: Hu, X. / Zhao, J. / Degrado, W.F. / Binns, A.N.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Multiple sugar-binding periplasmic receptor ChvE
B: Multiple sugar-binding periplasmic receptor ChvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1254
Polymers71,7372
Non-polymers3882
Water13,601755
1
A: Multiple sugar-binding periplasmic receptor ChvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0632
Polymers35,8681
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Multiple sugar-binding periplasmic receptor ChvE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0632
Polymers35,8681
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.488, 130.488, 63.422
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Multiple sugar-binding periplasmic receptor ChvE


Mass: 35868.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: AGR_C_4267, Atu2348, chvE / Plasmid: pJZ01 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL21(DE3) / References: UniProt: P25548
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 31% PEG4000, 0.2M Magnesium chloride, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 58954 / % possible obs: 79 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 21
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 1186 / Rsym value: 0.543 / % possible all: 62.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.477 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.08 / σ(I): 0 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2864 5.07 %random
Rwork0.1561 ---
obs0.158 56517 90.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.903 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8717 Å2-0 Å20 Å2
2---0.8717 Å20 Å2
3---1.7434 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5024 0 26 755 5805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045233
X-RAY DIFFRACTIONf_angle_d0.8597110
X-RAY DIFFRACTIONf_dihedral_angle_d13.3851936
X-RAY DIFFRACTIONf_chiral_restr0.061812
X-RAY DIFFRACTIONf_plane_restr0.004929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.81270.30441560.24823317X-RAY DIFFRACTION56
1.8127-1.88530.26422500.20864401X-RAY DIFFRACTION75
1.8853-1.97110.23652630.18115272X-RAY DIFFRACTION90
1.9711-2.0750.20963090.16315597X-RAY DIFFRACTION95
2.075-2.2050.19663100.15515669X-RAY DIFFRACTION97
2.205-2.37520.19482880.14995832X-RAY DIFFRACTION98
2.3752-2.61430.2033340.15435785X-RAY DIFFRACTION99
2.6143-2.99250.20243240.16515856X-RAY DIFFRACTION100
2.9925-3.76990.18422990.14585935X-RAY DIFFRACTION100
3.7699-45.4920.15543310.13315989X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.43280.3866-0.92291.4209-0.27751.09810.31140.5391-0.4264-0.37320.3220.02490.22080.0313-0.41540.2117-0.0096-0.03070.178-0.01520.0841-69.568813.2411-17.8901
20.8866-0.07360.03890.1829-0.1860.1970.0028-0.0416-0.2930.0533-0.0185-0.08160.14960.0818-0.030.10250.0091-0.00650.028900.0974-65.18838.2937-1.1737
30.91920.2080.83951.2227-0.17013.03760.00480.2836-0.3115-0.26490.14540.43480.1254-0.4831-0.1180.1637-0.0377-0.04240.1504-0.0090.1785-75.0099.1117-13.8393
41.190.4660.17670.6390.50971.6440.11410.2375-0.2358-0.10720.1264-0.29630.02780.2803-0.23540.08160.0070.00120.1156-0.04990.1428-55.754311.9303-9.7815
51.6098-0.32391.6371.6653-1.63322.73390.09630.41720.0126-0.24790.11060.22370.35070.4479-0.15480.1469-0.0053-0.02160.1728-0.00450.0889-64.123716.8804-17.8333
61.06920.994-0.31361.48660.22121.04760.01130.17030.0481-0.10740.1818-0.0794-0.2360.0808-0.13970.0885-0.0130.02840.0741-0.00660.0726-57.715622.7763-11.1357
70.45410.08130.11530.6709-0.36950.78540.0577-0.00210.03580.14610.0305-0.0366-0.1801-0.0542-0.06950.14870.01030.00840.0462-0.00110.0676-67.500422.30867.1694
81.0295-0.17440.21540.5709-0.28380.1579-0.4002-0.17960.04810.2167-0.0350.44990.0008-0.57590.40570.62750.0740.00210.4273-0.12190.1684-72.613822.440734.7993
90.0299-0.1838-0.050.61290.03191.01770.0586-0.10060.02990.2851-0.0285-0.3202-0.25240.16070.07460.2446-0.032-0.05540.0917-0.00730.1113-61.39122.361716.3812
100.88250.17040.00540.6584-1.13272.45790.02010.06660.23070.6448-0.0507-0.2489-0.7727-0.04060.18070.5955-0.0644-0.15890.1119-0.02320.1465-61.311125.91629.2759
110.7807-0.24650.7281.07690.18262.22030.01080.01220.05020.40470.0157-0.4903-0.11860.63570.00620.2324-0.0438-0.13770.1418-0.00990.2104-52.460115.185119.035
121.123-0.8906-0.13480.80980.03560.0679-0.0671-0.13650.05420.36390.1608-0.24440.0380.2756-0.03740.2754-0.0168-0.08530.1098-0.00110.0964-59.893411.90223.3639
130.95820.7706-0.25641.79520.49012.58580.0131-0.0474-0.2740.56690.2289-0.55530.98790.1801-0.14860.5297-0.0023-0.1930.05640.02520.1368-60.01534.019230.0244
140.4262-0.18890.21340.7038-0.70890.73220.0642-0.0401-0.11540.20590.0090.03370.06320.0748-0.07110.153-0.0054-0.00940.05520.01730.0698-69.80267.834215.3209
150.0461-0.31730.30072.0418-2.05044.27640.04220.07940.0082-0.0260.11670.4098-0.2856-0.3706-0.11060.08860.0176-0.02270.09470.00490.1167-76.079417.2636-6.6602
162.94450.0145-0.13654.13411.19713.88520.01260.6290.0284-0.9124-0.16820.514-0.5183-0.50960.06550.23720.0481-0.01710.16850.02850.0941-76.53825.915-10.4004
173.40091.9965-1.1262.43270.08070.80840.44310.12160.79450.31780.01210.3318-0.2664-0.12530.25150.16820.01640.0891-0.02010.00740.1147-66.189932.14561.2891
181.22450.9823-0.63981.4019-0.86740.49350.1737-0.29990.30720.0094-0.1380.2501-0.08150.0814-0.05990.16050.0290.04530.07340.01220.1276-70.173627.5227-0.6621
190.4575-0.4422-0.27880.6194-0.11630.44390.0524-0.028-0.21370.1605-0.0040.13990.0629-0.1216-0.04690.1439-0.01350.0160.07380.02280.1238-78.47126.541113.4033
202.7732-0.8238-0.31450.36850.433.28560.2173-0.4938-0.13540.45090.36830.00150.49630.0844-0.49850.21490.0141-0.03880.07150.0040.3224-75.9498-4.920510.7973
210.8687-0.40630.42541.88890.22590.43360.05990.2289-0.2568-0.41310.02310.14640.02730.0526-0.02760.17450.0312-0.02280.12810.00440.1431-89.796411.70665.9461
221.80420.5572-0.72111.629-2.87815.48840.0567-0.0746-0.9282-0.74280.0683-0.05651.41740.3047-0.00340.45210.098-0.05210.1229-0.09230.355-89.75061.68430.4664
231.1675-0.70760.64442.5511-0.57340.42380.07580.25950.0519-0.2295-0.072-0.27510.09070.16640.00560.2030.0216-0.00350.18120.02130.1723-88.747619.21571.9031
242.5928-2.18641.07882.956-1.22950.5690.38910.8703-0.0285-1.1266-0.6813-0.64340.22980.42020.24370.42480.09080.03240.31220.00840.1881-91.488719.4979-7.6949
250.75250.49340.83790.37650.55761.84320.15170.1023-0.07170.0522-0.00980.05310.2364-0.022-0.14590.15350.0307-0.04440.15730.00870.1825-97.073721.3784.1975
262.8623-1.09090.49342.73770.03140.15810.19260.78690.1416-0.9645-0.09350.4481-0.5125-0.04150.00060.3680.0942-0.11480.31130.03610.1827-100.588524.0552-6.1908
270.4622-0.15820.02221.3219-0.55780.34320.07920.1858-0.2952-0.12990.02740.67450.0019-0.163-0.10540.18260.0578-0.06250.1682-0.0120.2873-103.066316.6565.038
280.7015-0.61880.54711.489-1.37072.4807-0.1737-0.5497-0.66870.19860.64750.37450.2073-0.8124-0.46560.26870.11330.10660.36750.22750.3629-104.687411.345629.154
290.32980.25530.20140.63280.17950.12350.05310.15420.03390.12990.25260.1666-0.0258-0.1245-0.17180.69850.28410.43721.08640.42340.7264-108.9910.938843.4012
302.62360.06970.58090.5056-0.4230.7566-0.2137-0.7323-0.03880.38250.19090.3027-0.4485-0.4903-0.05920.30570.190.09090.3680.06970.2349-105.404821.038328.4169
312.04150.8766-0.15012.3194-0.3493.35-0.1439-0.63260.18440.4634-0.12760.6697-0.4656-0.75460.23650.4140.22450.09980.462-0.02360.3247-104.39927.074334.0736
320.50240.07480.34970.1510.36310.7209-0.337-0.22790.30840.50380.0579-0.1244-0.30220.05720.23940.37320.0809-0.06850.15120.0040.2178-92.710327.880828.1585
330.67210.177-0.75970.19470.61595.26540.2876-0.88990.4979-0.2839-1.82870.51611.39610.53261.27080.94540.1022-0.15290.6264-0.08660.1737-95.242326.370945.063
341.6733-1.09510.60041.8924-1.03740.7571-0.3875-0.4118-0.03820.58990.1634-0.0651-0.3238-0.23020.06250.39540.1283-0.01930.17780.06010.1406-90.39915.204233.5346
351.0334-0.84740.38891.0918-0.73580.9522-0.0081-0.0799-0.36420.0530.09940.38280.2174-0.1284-0.18440.1810.0302-0.01540.08490.05190.2392-95.62736.053117.5234
361.94540.13610.5310.41950.53422.52340.35840.8475-0.2243-0.46080.15350.64350.456-0.4435-0.35780.45220.0523-0.25870.3618-0.0980.5057-104.84895.1676-3.0495
370.26390.59670.22342.3345-0.24091.40410.5040.1172-0.479-0.2111-0.15540.32830.3255-0.2558-0.42390.14980.0468-0.00710.2120.09420.5415-112.443914.861610.0859
381.03250.13290.68760.81330.4491.11030.2570.0009-0.5538-0.0890.08230.89690.3682-0.0778-0.37150.19880.0264-0.04480.16080.09650.4759-105.065310.444314.0649
394.89720.7259-0.45790.3836-1.0253.4350.077-0.1189-1.05490.46090.23790.44430.5544-0.235-0.12150.28620.00850.0250.07250.16430.4191-91.9299-2.221625.7027
403.5516-2.29640.81511.7006-0.45410.32640.3387-0.2274-0.9762-0.0952-0.12070.49710.142-0.1943-0.26110.21890.014-0.01110.11460.06020.2918-83.28160.773122.376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:8)
2X-RAY DIFFRACTION2(chain A and resid 9:26)
3X-RAY DIFFRACTION3(chain A and resid 27:35)
4X-RAY DIFFRACTION4(chain A and resid 36:57)
5X-RAY DIFFRACTION5(chain A and resid 58:63)
6X-RAY DIFFRACTION6(chain A and resid 64:86)
7X-RAY DIFFRACTION7(chain A and resid 87:125)
8X-RAY DIFFRACTION8(chain A and resid 126:131)
9X-RAY DIFFRACTION9(chain A and resid 132:157)
10X-RAY DIFFRACTION10(chain A and resid 158:172)
11X-RAY DIFFRACTION11(chain A and resid 173:200)
12X-RAY DIFFRACTION12(chain A and resid 201:219)
13X-RAY DIFFRACTION13(chain A and resid 220:235)
14X-RAY DIFFRACTION14(chain A and resid 236:265)
15X-RAY DIFFRACTION15(chain A and resid 266:277)
16X-RAY DIFFRACTION16(chain A and resid 278:288)
17X-RAY DIFFRACTION17(chain A and resid 289:294)
18X-RAY DIFFRACTION18(chain A and resid 295:305)
19X-RAY DIFFRACTION19(chain A and resid 306:324)
20X-RAY DIFFRACTION20(chain A and resid 325:330)
21X-RAY DIFFRACTION21(chain B and resid 2:26)
22X-RAY DIFFRACTION22(chain B and resid 27:31)
23X-RAY DIFFRACTION23(chain B and resid 32:52)
24X-RAY DIFFRACTION24(chain B and resid 53:61)
25X-RAY DIFFRACTION25(chain B and resid 62:72)
26X-RAY DIFFRACTION26(chain B and resid 73:85)
27X-RAY DIFFRACTION27(chain B and resid 86:106)
28X-RAY DIFFRACTION28(chain B and resid 107:124)
29X-RAY DIFFRACTION29(chain B and resid 125:130)
30X-RAY DIFFRACTION30(chain B and resid 131:164)
31X-RAY DIFFRACTION31(chain B and resid 165:176)
32X-RAY DIFFRACTION32(chain B and resid 177:199)
33X-RAY DIFFRACTION33(chain B and resid 200:205)
34X-RAY DIFFRACTION34(chain B and resid 206:253)
35X-RAY DIFFRACTION35(chain B and resid 254:273)
36X-RAY DIFFRACTION36(chain B and resid 274:286)
37X-RAY DIFFRACTION37(chain B and resid 287:293)
38X-RAY DIFFRACTION38(chain B and resid 294:311)
39X-RAY DIFFRACTION39(chain B and resid 312:322)
40X-RAY DIFFRACTION40(chain B and resid 323:330)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more